6-170318393-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032448.3(FAM120B):c.1003G>A(p.Ala335Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,614,070 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120B | NM_032448.3 | c.1003G>A | p.Ala335Thr | missense_variant | 2/11 | ENST00000476287.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.1003G>A | p.Ala335Thr | missense_variant | 2/11 | 1 | NM_032448.3 | A2 | |
FAM120B | ENST00000537664.5 | c.1072G>A | p.Ala358Thr | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000630384.2 | c.1039G>A | p.Ala347Thr | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000625626.1 | c.-90+11551G>A | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251280Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135816
GnomAD4 exome AF: 0.000175 AC: 256AN: 1461756Hom.: 1 Cov.: 35 AF XY: 0.000199 AC XY: 145AN XY: 727150
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | The c.1003G>A (p.A335T) alteration is located in exon 2 (coding exon 1) of the FAM120B gene. This alteration results from a G to A substitution at nucleotide position 1003, causing the alanine (A) at amino acid position 335 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at